Graphene on silicon carbide (SiC) bears great potential for future graphene electronic applications because it
is available on the wafer scale and its properties can be custom tailored by inserting various atoms into the graphene/SiC interface. It remains unclear, however, how atoms can cross the impermeable graphene layer during this widely used intercalation process. Here we demonstrate that in contrast to the current consensus, graphene layers grown in argon atmosphere on SiC are not homogeneous, but instead are composed of domains of different crystallographic stacking as they have been observed in other systems. We show that these domains are the AB and AC versions of Bernal stacking, that they are intrinsically formed during growth and that dislocations between domains dominate the (de)intercalation dynamics of hydrogen. Tailoring the resulting dislocation networks, e.g., through substrate engineering, will increase the control over the intercalation process and could open a playground for topological and correlated electron phenomena on the wafer scale.